Visualizing VCF files

The goal is to visualize the data in a VCF file.

This project is tracked by ticket [#224]

The basic code for indexing/reading VCF files is already in JAnnot (VCFWrapper).

Steps that need to be completed:

JAnnot

• make parser more robust
• make abstractions for types of variation events
• make test cases to support above two points
• Benchmark speed on large files

GenomeView

• implement new visualization tracks that gives useful information about the variations in a VCF file

Sample VCF

Sample VCF file and instructions on how to get them loaded. This needs to be expanded here and when released moved to the user documentation.

Download (small)example VCF file:
ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/release/2010_07/trio/snps/CEU.trio.2010_03.genotypes.vcf.gz

and the corresponding index file
ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/release/2010_07/trio/snps/CEU.trio.2010_03.genotypes.vcf.gz.tbi

-> Load file in GV.